I'm sure this is a noobish question, but I want to make sure I don't screw anything up right off the bat

Going through the TSLPatcher Readme, it says the following for setting up your mod...

2.4.Copy all the files that belong to your MOD into the tslpatchdata folder.

2.5.Extract UNALTERED copies of any 2DA and standard game GFF format files you want the TSLPatcher to work with. These files will be copied to override and then modified if the file did not already exist in the user's override folder. Put these files in the tslpatchdata folder.

Now, I'm not doing any new content or anything for this mod. Just some edits to existing .2da's and items. That's all I can actually do right now, being a modding newb. So my modded file names are identical to the unaltered ones. If I try to do the above, one set of files will just overwrite the other, since they have the same file names.

What am I missing? Does 2.4 above only apply to NEW files your mod adds, and I should just add the unaltered copys to the folders if I'm just editing? Or am I supposed to create a sub-folder inside "tslpatchdata" for one set?